MolNFT v1 · #139204 · protein
Ternary complex structure of a double mutant I454RA456K of O- succinylbenzoate CoA synthetase (mene) from bacillus subtilis bound with AMP and its product analogue osb-ncoa at 1.76 ångström
5X8F · 2-succinylbenzoate--CoA ligase: “Ternary complex structure of a double mutant I454RA456K of O- succinylbenzoate CoA synthetase (mene) from…”. X-ray diffraction, 5 ligands (S0N, AMP, NA), 20 pockets (best druggability 0.84). MolNFT…
- PDB
- 5X8F
- Type
- protein
- Length
- 1,936 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-succinylbenzoate--CoA ligase
- EC
- 6.2.1.26
- UniProt
- P23971
- Ligands
- S0N, AMP, NA, MG, CA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-succinylbenzoate--CoA ligase (EC 6.2.1.26) | protein | 483 | 31% helix, 30% strand | P23971 |
| B | 2-succinylbenzoate--CoA ligase (EC 6.2.1.26) | protein | 485 | 32% helix, 30% strand | P23971 |
| C | 2-succinylbenzoate--CoA ligase (EC 6.2.1.26) | protein | 484 | 32% helix, 30% strand | P23971 |
| D | 2-succinylbenzoate--CoA ligase (EC 6.2.1.26) | protein | 484 | 31% helix, 30% strand | P23971 |
Ligands and binding sites
- S0N · o-succinylbenzoyl-N-coenzyme A · ligand · 4 copies · chains A, B, C, D
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, C
- NA · Sodium ion · metal · 33 copies · chains A, B, D, C
- MG · Magnesium ion · metal · 27 copies · chains A, B, D, C
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.84 | 0.85 | 126 | S0N, MG, NA |
| 2 | 997 | 0.84 | 0.85 | 124 | S0N, AMP, MG |
| 3 | 968 | 0.83 | 0.84 | 121 | S0N, AMP, MG, NA |
| 4 | 849 | 0.82 | 0.84 | 106 | S0N, NA |
| 5 | 635 | 0.69 | 0.77 | 61 | MG, NA, CA |
Interfaces
4 interfaces between chains.
- B–D · 1283 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1228 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 300 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 92 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5X8F · Ternary complex structure of a double mutant I454RA456K of o-Succinylbenzoate CoA… · the same entry in another collection · chain D against D, TM-score 1.00
- P23971 · AlphaFold monomer V2.0 prediction for 2-succinylbenzoate--CoA ligase (P23971) · a predicted model of the same protein · chain C against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P23971
- Elsewhere: RCSB PDB 5X8F · PDBe 5X8F · UniProt P23971
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